Amplifying Trouble

© Pascal Goetgheluck / Photo Researchers, Inc.

PCR, in one form or another, has become fairly routine. It's used for everything from cloning and mutating, to analyzing RNA expression, to identifying fossils and criminals. Tools for conducting standard PCR, real-time PCR (RT-PCR), and quantitative PCR (qPCR) have followed suit, and there are Web sites for designing and ordering primers or purchasing off-the-shelf kits. These days, it's just a matter of adding reagents and nucleic acids to a tube or plate, pushing "start," and checking the computer a little while later to look at your results.

Sometimes things don't go as smoothly as the protocols would suggest. Target sequences might be shorter than the protocols can handle. Primers can dimerize, or they might not amplify a unique product. The samples themselves might be difficult to isolate: Maybe they're degraded or cross-linked, or maybe they're contaminated with the DNA of unrelated organisms or, worse yet, related organisms.

Whatever the issue, chances are good that you're not alone in your woes. Researchers like to share their war stories about amplifications gone wrong, but fortunately, they also share stories about how to troubleshoot PCR problems or avoid problems altogether. The Scientist tracked down a few cases of dodgy PCR gone right -- read about them by clicking on the PCR user profiles in the yellow box above.